[gmx-users] bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

I am trying to implement dihedral restraints for lipids in a bilayer using what is suggested here: http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints However, although the dihedral angles seem to be restrained fine, the leaflets move apart by 10s of nanometers along +z over a nanose

[gmx-users] Postdoc and PhD positions in Denmark

University of Southern Denmark, Odense immediately in the group of Dr. Himanshu Khandelia (www.memphys.sdu.dk/~hkhandel). The successful candidate will work in a highly collaborative atmosphere at the Center for Biomembrane Physics MEMPHYS (www.memphys.sdu.dk) together with theorists and

[gmx-users] postdoctoral position in computational biophysics in Denmark

A postdoctoral position in simulations of membranes and membrane proteins is available from 1 December 2013 (starting date flexible) for one year (with possible extension) at the University of Southern Denmark (SDU), Odense in the group of Dr Himanshu Khandelia. Knowledge of statistical physics

[gmx-users] Gromacs 4.0.4 problem in extending MARTINI run by 600 ns, but no problem extending run by 60 ns using tpbconv

Dear All, I have run into this problem while using tpbconv. I typically write a new set of output files every ~ 600 ns. However, after about 108 repeats, tpbconv fails to write a new .tpr file: ### tpbconv -s poptocg25-108.tpr -extend 60 -o poptocg25-109.tpr ... ... Reading t

[gmx-users] uniform neutralizing plasma for PME

Is there an implementation in gromacs for using a uniform neutralizing plasma with PME, to avoid use of counterions? Thank you -Himanshu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search

[gmx-users] Uniform neutralizing plasma for Particle Mesh Ewald (PME) instead of counterions

Is there an implementation in gromacs for using a uniform neutralizing plasma with Particle Mesh Ewald (PME), to avoid use of counterions? Thank you -Himanshu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/

[gmx-users] GROMACS performance on 10 GBit/s or 20Gbit/s infiniband

We are buying a new cluster with 8-code nodes and infiniband, and have a choice between 10 Gbit/s and 20 Gbit/s transfer rates between nodes. I do not immediately see the need for 20GBit/s between nodes, but thought it might be worthwhile to ask for the experts' opinions regarding this? Is the

[gmx-users] What is the block size in the -ee option of g_analyze

I was wondering how gromacs decides on the block size to be used when using g_analyze to calculate block errors? There does not seem to be an option where the user can set it ? Thank you -Himanshu Himanshu Khandelia, PhD, Research Assistant Professor (Postdoc

[gmx-users] How does GROAMCS handle PME with non-zero charge

Hi, How does GROMACS handle PME calculations if the system has non-zero charge. Does it automatically apply a neutralizing charge density ? Thank you -Himanshu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinf

[gmx-users] GROMACS 4.0.2 error Value of 'multiplicity' in Proper Dih. is 0,

r the help, -Himanshu ---- Himanshu Khandelia, PhD, Research Assistant Professor (Postdoc), MEMPHYS, Center for BioMembrane Physics: www.memphys.sdu.dk University of Southern Denmark (SDU) Campusvej 55, Odense M 5230, Denmark Phone: +45 6550 3510, +45 2398 7972 Fax: +45 6550

[gmx-users] Re: GROMACS 4.0.2 error Value of 'multiplicity' in Proper Dih. is 0

lt;496cdf33.6070...@xray.bmc.uu.se> Content-Type: text/plain; charset=ISO-8859-1; format=flowed himanshu khandelia wrote: Hi, I am using grompp after installing gromacs 4.0.2, and get the following error for a single lipid molecule: ---

[gmx-users] Invitation to connect on LinkedIn

LinkedIn himanshu khandelia requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - himanshu View invitation from himanshu khandelia http://www.linkedin.

[gmx-users] selecting multiple groups while using analysis routines like trjconv

Hi, While using trjconv and the like, it is possible to select multiple groups and write out their trajectory (for example, proteins AND ions) ? Or does one have to write a new index file to be able to do this ? Thank you very much, -Himanshu ___ gmx-

[gmx-users] gromacs analysis performance on a dual core suse box.

Hello, I am using a dual core Xeon with 4 GB RAM to do some gromacs analysis and want to know what is the limiting factor in my machine's performance. When I run, say, a trjconv command on a 2.3 GB trajectory, the rest of my machine pretty much freezes up. A trjconv will use only 1 cpu, but is it

[gmx-users] problem with simulation of phosphatidic acid, possibly in my topology?

Hi, I am trying to run a simulation of a POPC bilayer mixed with some mono-anionic Phosphatidic acid (POPA) , where the choline group is replaced by a hydrogen atom. However, the energy of my simulation box diverges, and I am trying to fix the problem. I also tried running a simulation of PA solva

[gmx-users] Re: problem with simulation of phosphatidic acid, possibly in my topology?

PS: My previous email was accidentally sent from the gmail account of my colleague, who uses the same workstation. My apologies. This is just a disclaimer on her behalf. On Mon, May 5, 2008 at 11:34 AM, himanshu khandelia <[EMAIL PROTECTED]> wrote: > Hi, > > I am trying to run

[gmx-users] g_density problem segmentation fault glibc detected

Hi, I am trying to calculate the density in a bilayer simulation: echo 27 | g_density -f lipiddrg.xtc -n all.ndx -s all.tpr -o head.xvg -sl 200 -b 4 The system size is about 6.5 x 6.5 x 9.6 I get the following error, after g_density has read most of the trajectory: *** glibc detected *** g

[gmx-users] So how is the terminal methyl order parameter calculated, and about unsaturated carbons ?

Hi, As I understand it, g_order does not report the order parameter for the terminal methyl carbon because the C-H bond is missing for united atoms. So, how do people calculate the order parameter for the terminal methyl atom from GROMACS simulations? I see it reported in articles all the time. Co

[gmx-users] g_spatial installation problem. Points to g_cluster?

Hi I was trying to install Chris Neale's g_spatial, and followed the nstructions in the readme. However, g_spatial seems to point to g_cluster before and after the make install ?? Does anyone have any pointers? I am trying installing on version 3.3.2 thank you -himanshu

Re: [gmx-users] Large VCM error for a POPC bilayer simulation : 2nd attempt

assembly was not done using genconf. I was wondering how to get past the large VCM error ? Thank you -Himanshu On 10/17/07, Rainer Böckmann <[EMAIL PROTECTED]> wrote: > > Hi, > > genconf -nbox 2 2 1 > > will help you. > > Best, > rainer > > > himanshu k

Re: [gmx-users] Large VCM error for a POPC bilayer simulation : 2ndattempt

Hi, The simulation does not explode if I run in NVT for 5000 steps. I am running a longer simulation now, and will update the post. If this does not work, I will try editconf. Thank you all for the comments and help, -Himanshu On 10/17/07, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > > >

[gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel

Hi This question is about trying to make sure that I am doing the right thing while trying to use tpbconv to restart jobs. After minimization, for the first dynamics run, I use gen_vel = yes. For subsequent restart runs however, gen_vel must be set to no. After the first dynamics run of 200ps, my

Re: [gmx-users] restarting jobs using tpbconv and grompp : with regards to gen_vel

> Check out http://wiki.gromacs.org/index.php/Doing_Restarts Thanks very much. I do understand the general restarting mechanism. It is only the first restart that was a little bit confusing > > > I just wanted to confirm if what I am doing makes sense ? Thanks very > > much for the help ! > > T

[gmx-users] No improvement in scaling on introducing flow control

Hi, We tried turning on switch control on our local cluster (www.dcsc.sdu.dk) but were unable to achieve any improvement in scale up whatsoever. I was wondering if you folks could shed light upon how we should go ahead with this. (We have not installed the all-to-all patch yet) The cluster archit

Re: [gmx-users] No improvement in scaling on introducing flow control

odes with 2 CPUs sharing one > NIC were faster than nodes with 4 CPUs sharing two NICs. Could be > on-node contention, since both interfaces probably end up on the same > bus internally. > > Regards, > Carsten > > > himanshu khandelia wrote: > > Hi, > > > &g

[gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????

Hi I seem to be doing something wrong here, but cannot figure out what. - I have run a 200 ps NVT simulation for a lipid bilayer on 4 processors using the gromacs-3.3.1 build. - The last frame from the NVT simulation was used in conjunction with a newly written .mdp file to restart the simulati

Re: [gmx-users] NVT to NPT. Works on a single processor, does not work on 4 ????

Thanks for the reply. But why the difference between the 4-cpu and the 1-cpu ? On 10/27/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > > Hi > > > > I seem to be doing something wrong here, but cannot figure out what. > > > > - I have run a 200 ps NVT simulation for a lipid bilayer on 4 > > process

Re: [gmx-users] No improvement in scaling on introducing flow control

Hi Carsten, The benchmarks were made is 1 NIC/node, and yet the scaling is bad. Does that mean that there is indeed network congestion ? We will try using back to back connections soon, -himanshu maybe your problem is not even flow control, but the limited network bandwidth which is shared am

Re: [gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

because how openmpi allocates cpus also depends on what options gromacs was originally compiled with (in connection to MPI). So its not strictly a 100% openmpi question. Thanks for the help -Himanshu On Nov 2, 2007 3:07 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > himanshu khandelia wrot

[gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

Hi, I am requesting 2 4-cpu nodes on a cluster using PBS. I want to run a separate GMX simulation on each 4-cpu node. However, on 2 nodes, the speed for each simulation decreases (50 to 100%) if compared to a simulation which runs in a job which requests only one node. I am guessing this is becaus

Re: [gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

how either, but just seemed logical to me. I may be wrong On Nov 2, 2007 4:28 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > himanshu khandelia wrote: > > Hi Mark, > > > > I do not want to request two separate 1-node jobs, so that I can make > > maximum use of the M

Re: [gmx-users] Node assignment using openmpi for multiple simulations in the same submission script in PBS

My apologies for not reading the reference properly. Thanks, Mark However, the --byslot option is not being able to do the needful. I will update if I learn something new. On Nov 2, 2007 11:50 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > himanshu khandelia wrote: > > I get bad

[gmx-users] protein residue numbering not retained in GROMACS ?

According to the documentation and the mailing lists, it seems that protein residue numbering is not retained in gromacs, is that correct ? No way to go around this ? There are, of course, obvious advantages of retaining residue numbers from pdb files. Thank you -Himanshu ___

Re: [gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx

Or if can use GROMOS87 for the protein and the Berger for the lipids, correct ? On Nov 8, 2007 12:49 PM, Erik Lindahl <[EMAIL PROTECTED]> wrote: > Hi, > > On Nov 7, 2007, at 5:40 PM, maria goranovic wrote: > > > Thanks for the help, David. Actually, I just realized I was trying to > > decide based

Re: [gmx-users] water in lipid bilayer

> I already constrained the waters in the z-direction > at the start of the simulation, so that didn't work in this case. This happened to me as well. Try increasing the force constants on water by an order of magnitude. ___ gmx-users mailing listgm

Re: [gmx-users] water in lipid bilayer

AIL PROTECTED]> wrote: > Do you mean constrain the force constants just in the z-direction? Keep in > mind that the water is already in the gap, so it's now a matter of getting > it out. Would constraining water in any direction accomplish this? > > Thanks, > > Max > > >

[gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp

from final.gro will be ignored ###### On Nov 30, 2007 3:30 PM, himanshu khandelia <[EMAIL PROTECTED]> wrote: > Hi Folks, > > I am not being able to debug a little problem. I hope someone will be > able to point out the mistake. Here is what I am trying to do: > > I need

[gmx-users] Problem in atom name correspondence between protein topology and coordinates after mutation grompp

Hi Folks, I am not being able to debug a little problem. I hope someone will be able to point out the mistake. Here is what I am trying to do: I need to mutate a SER to a GLU residue in a protein. However, after mutation (and making a new topology), when I run grompp, I get the following error:

[gmx-users] non-zero potential in pure POPC bilayer Odd profile across bilayer

Hi, I calculated the electrostatic potential using g_potential across a large 416-lipid POPC bilayer from a 200 ps trajectory. The bilayer is well-hydrated, and has zero charge. However, I get a very odd potential which starts off at 0.0 and ends at 0.6 V, but is not monotonically increasing all

Re: [gmx-users] non-zero potential in pure POPC bilayer Odd profile across bilayer

ayers are not equivalent which is probably > due to lack of equilibration. > You can convince yourself by measuring the density of the system along the > axis normal to the bilayer (use g_density -h). > > Regards. > > Pedro. > > > > 2007/12/3, himanshu khandeli

[gmx-users] Installation problems of an mpi version on SUSE 10.2

Hi, I installed a serial version of GMX, and am trying to install an mpi version. I did a make distclean, and followed standard procedures, and am getting the following errors during make mdrun: Any suggestions ? Thank you ! ## (cd ./sr